[eluser]Simian Studios[/eluser]
Depends exactly what you want to do really.. what you could do is have some controller methods set up that render different parts of the page through their views.
Then, in your JS, you call the functions via an AJAX request and update the client with the response from the server - that way you could for example use the node builder to build an element that you then update with content via the AJAX requests.
Although, the question has to be asked why you're doing it that way specifically? I always try to build so that the app works without JS, and then the JS sits on top and enhances the behaviour, rather than being a vital ingredient.